Using Boolean Wraps texture awkwardly
I don't know why your head object is acting so strangely with the Boolean modifier. The proper setting for the Boolean is "Intersect" in order to get the cubes to cut holes in the head:  



However, I don't know why the body disappears. So, here is a work-around:  


First, delete the back vertices of the cubes you're going to use to cut out the eye holes so they are just rectangles, like this:  

  
Then go into Front Ortho view (front view with Numpad 1, ortho view with Numpad 5):  

  
Now first select the rectangles, then hold down SHIFT and also select the player, so that both are selected together. 
Now, press TAB to go into Edit mode, then in the Tools panel, in the Tools tab, click on Knife Project:  

  

This will cut holes in the face of the player. 
Now select the vertices of the newly-made eye sockets and extrude them back along the Y axis:  

  
Now select the back-most vertices of one eye socket and then press F to make a face there. Then do the same thing for the other eye socket: